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PanPhlAn / Download_and_Installation

PanPhlAn - Download and Installation

Download the PanPhlAn software

a) Download by using wget

mkdir panphlan
mv CibioCM-panphlan-*/panphlan_* panphlan/

b) or by using the Mercurial hg command

hg clone

→ version history


PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be installed on your system:

  • Python version 2.7 or 3.x (including the Biopython module, numpy, and matplotlib)
  • bowtie2
  • samtools
  • usearch 7 (only for generating your own species database)

Add the paths of your installed tools to your .bashrc file

export PATH=/your/path/to/samtools/:$PATH
export PATH=/your/path/to/bowtie2/bowtie2-2.1.0/:$PATH
export BT2_HOME=/your/path/to/bowtie2/bowtie2-2.1.0/
export BOWTIE2_INDEXES=/your/path/to/PanPhlAn_DB/and/bowtie2_indexes/

Download a species pangenome database

Pangenome databases are available for more than 400 species: → download page

Next steps

  1. Generate a user-specific pangenome database of a bacterial species, or download a pre-processed database
    → panphlan_pangenome_generation

  2. Screen your metagenomic samples for species related genes by mapping against the species database.
    → panphlan_map

  3. Merge and process the mapping results to get the final gene-family presence/absence profiles of all detected strains.
    → panphlan_profile